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Systematic benchmarking of tools for structural variation detection using short- and long-read sequencing data in
Sang He1,2, Bangmin Song1, Yueting Tang1
1Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China.
Evaluating structural variation (SV) detection in pigs, this study found long-read sequencing platforms superior for identifying SVs missed by short-read methods. SVIM-asm demonstrated optimal performance for SV calling in farm animals.
Area of Science:
- Genomics
- Comparative Genomics
- Bioinformatics
Background:
- Accurate detection of structural variations (SVs) is crucial for understanding genetic diversity and disease in livestock.
- Existing SV detection tools employ diverse algorithms, necessitating comparative performance evaluation.
Purpose of the Study:
- To systematically evaluate the performance of various SV detection programs in pigs.
- To establish a benchmark SV set for pigs to assess tool accuracy.
- To provide guidance for optimal SV calling pipelines in farm animals.
Main Methods:
- Sequencing of five genetically diverse pig breeds using both short- and long-read DNA sequencing platforms.
- Creation of breed-specific SV benchmark sets.
- Performance assessment of 16 SV calling tools using the benchmark sets.
Main Results:
- Long-read sequencing platforms identified numerous SVs missed by short-read platforms with comparable precision.
- The assembly-based tool SVIM-asm exhibited superior SV detection performance and resource efficiency.
- SVs with higher read support, smaller sizes (<1 kb), and located outside repetitive regions showed higher detection accuracy.
Conclusions:
- Long-read sequencing is highly effective for comprehensive SV detection in pigs.
- SVIM-asm is a recommended tool for SV calling in pigs and potentially other farm animals.
- Understanding SV characteristics (read support, size, location) aids in accurate detection.
